The Free Energy Landscape of Retroviral Integration and Molecular Mechanisms of DNA Compaction

Abstract

Retroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the retroviral replication cycle. Despite its importance, many mechanistic details remain poorly understood. Using prototype foamy virus (PFV) as a model system, we monitor target DNA binding, the ensuing strand transfer reaction, and final complex disassembly by AFM imaging and magnetic tweezers force spectroscopy [1]. Our results reveal how multivalent target interactions at discrete auxiliary interfaces of the intasome render target capture irreversible, while allowing dynamic site selection. Strand transfer results in allosteric conformational changes and an extremely stable strand transfer complex [1]. Building upon the results on the model system, we investigate human immunodeficiency virus (HIV) pre-integration complexes (PICs). HIV must enter the nucleus to integrate the viral DNA genome. Nuclear import is complicated by the size restriction imposed by nuclear pore complexes that require compaction of the viral DNA within PICs. While the precise protein composition and DNA folding mechanism within PICs are unknown, the viral enzyme integrase is a major constituent of PICs. Whereas the strand transfer reaction involves an integrase multimer assembled at the viral DNA ends, PICs contain 10-fold more integrase monomers than required for catalysis. We therefore speculate on a functional role for integrase beyond catalysis and investigate whether integrase could serve a structural role in mediating DNA compaction in PICs. We again use atomic force microscopy imaging and magnetic tweezers-based micromanipulation to demonstrate that HIV integrase induces flexible bends and oligomerizes on DNA into particles capable of dynamic bridging and looping, which allow for the conformational plasticity that provides a route towards efficient compaction of the viral genome. [1] Vanderlinden, et al., Nature Comm. (2019).